In the year After Colony 196, one year after the conclusion of the intergalactic civil war, a state of stasis prevails over the Earth and its colonies. Seeing no further use for their Gundam mobile suits, war heroes Duo Maxwell, Heero Yuy, Trowa Barton, and Quatre Raberba Winner decide to destroy these weapons by launching them into the sun's surface.

Before the Gundam reach their destination, the universal peace is shattered by the emergence of Mariemaia Khushrenada—the only child of the former tyrannical aristocrat Treize. Mariemaia abducts diplomat Relena Peacecraft and announces plans to launch "Operation Meteor," with the intention of posthumously fulfilling Treize's world domination plot.

With the help of former enemy Zechs Marquise and his mobile suit Tallgeese, the heroic pilots must reacquire their mobile suits to wage one final battle against the Khushrenada dynasty, including fighting against their former ally Wufei Chang, now aligning himself with Mariemaia's ambitions.